Fig. 4

Differential gene expression (DGE) analysis. A Table as outputted from RStudio of the comparisons made for DGE analysis. Sham versus TBI comparisons yielded no differentially expressed genes, but the Male versus Female comparisons yielded a number of differentially expressed genes. B Histogram of P-values exhibit a uniform distribution for the Sham vs. TBI comparison, indicating no significant difference. C Histogram of P-values have a higher frequency at smaller significant P-values and a lower frequency at higher non-significant P-values for the Male vs. Female comparison, indicating a significant difference. D List of the 10 most differentially expressed genes from the Males versus Females comparison, all genes are located on sex chromosomes. E Stripchart of normalised log2 expression levels of individual samples for the most differentially expressed “Xist” gene (significant) in Males vs. Females, which is located on the X chromosome. F Stripchart of normalised log2 expression levels of individual samples for the most differentially expressed “Tbc1d19” gene (not significant) in Sham vs. TBI, which is a protein-coding gene located on chromosome 4 that is predicted to act as a GTPase activating protein. Plots in B, C, E and F were generated in RStudio